scholarly journals Relationship Between Drug Targets and Drug-Signature Networks: A Network-Based Genome-Wide Landscape

2021 ◽  
Author(s):  
Chaewon Lee ◽  
Sungmin Kim ◽  
Soonok Sa ◽  
Sang-Min Nam ◽  
Hyun Wook Han
Keyword(s):  
Drug Target ◽  
Drug Targets ◽  
Drug Effects ◽  
Network Models ◽  
Therapeutic Drug ◽  
Bipartite Network ◽  
Cellular Mechanisms ◽  
Target Network ◽  
Living Organisms ◽  
Approved Drugs

Abstract Drugs produce pharmaceutical and adverse effects that arise from the complex relationship between drug targets and signatures; by considering such relationships, we can begin to understand the cellular mechanisms of drugs. In this study, we selected 463 genes from the DSigDB database corresponding to targets and signatures for 382 FDA-approved drugs with both protein binding information for a drug-target score (KDTN, i.e., the degree to which the protein encoded by the gene binds to a number of drugs) and microarray signature information for a drug-sensitive score (KDSN, i.e., the degree to which gene expression is stimulated by the drug). Accordingly, we constructed two drug–gene bipartite network models, a drug-target network and drug-signature network, which were merged into a multidimensional model. Analysis revealed that the KDTN and KDSN were in mutually exclusive and reciprocal relationships in terms of their biological network structure and gene function. A symmetric balance between the KDTN and KDSN of genes facilitates the possibility of therapeutic drug effects in living organisms. These results provide new insights into the relationship between drugs and genes, specifically drug targets and drug signatures.

Proteome wide screening for identification of putative drug target gene in Nautella italica and structure-based ligand screening for therapeutic candidates

2021 ◽  
Vol 25 (12) ◽  
pp. 122-136
Author(s):  
Odumpatta Rajasree ◽  
Arumugam Mohanapriya
Keyword(s):  
Drug Target ◽  
Drug Targets ◽  
Three Dimensional ◽  
Opportunistic Pathogen ◽  
Dimensional Structure ◽  
Therapeutic Drug ◽  
Zinc Database ◽  
Delisea Pulchra ◽  
Toxicity Analysis ◽  
Potential Ligand

In silico based subtractive genomic approaches were employed to identify the key drug targets for an opportunistic pathogen Nautella italica, a member of the marine Roseobacter clade that causes bleaching disease in the temperate-marine red macro algae, Delisea pulchra. The aim of this study is to propose new active ligands against bleaching disease seen in algae. Using comparative and subtractive genomic approach, a set of 21 proteins were identified as the therapeutic drug target proteins for algal bleaching. This core set of drug targets has been analyzed for network topology using string network analysis and major hub gene identified by CytoHubba was rpoB (DNA directed RNA Polymerase subunit beta). The three-dimensional structure of rpoB was built by comparative modelling and used to perform a virtual screening of Zinc database by DOCK Blaster server. The 50 top scored compounds were screened for toxicity analysis by OSIRIS Data Warrior and ECOSAR tool. Further refinement by autodock program revealed two compounds ZINC49821385 and ZINC97218938 with the best binding energy of -7.07 and -6.79 respectively. These results indicated that 5-(4- isopropylphenyl)furan-2-carboxamide (ZINC ID 49821385) could be one of the potential ligand to treat bleaching disease in algae.

scholarly journals Comparison of FDA Approved Kinase Targets to Clinical Trial Ones: Insights from Their System Profiles and Drug-Target Interaction Networks

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Jingyu Xu ◽  
Panpan Wang ◽  
Hong Yang ◽  
Jin Zhou ◽  
Yinghong Li ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Comparative Analysis ◽  
Drug Target ◽  
Drug Targets ◽  
Therapeutic Potential ◽  
Interaction Networks ◽  
Therapeutic Area ◽  
Key Factors ◽  
Target Interaction ◽  
Approved Drugs

Kinase is one of the most productive classes of established targets, but the majority of approved drugs against kinase were developed only for cancer. Intensive efforts were therefore exerted for releasing its therapeutic potential by discovering new therapeutic area. Kinases in clinical trial could provide great opportunities for treating various diseases. However, no systematic comparison between system profiles of established targets and those of clinical trial ones was conducted. The reveal of probable difference or shift of trend would help to identify key factors defining druggability of established targets. In this study, a comparative analysis of system profiles of both types of targets was conducted. Consequently, the systems profiles of the majority of clinical trial kinases were identified to be very similar to those of established ones, but percentages of established targets obeying the system profiles appeared to be slightly but consistently higher than those of clinical trial targets. Moreover, a shift of trend in the system profiles from the clinical trial to the established targets was identified, and popular kinase targets were discovered. In sum, this comparative study may help to facilitate the identification of the druggability of established drug targets by their system profiles and drug-target interaction networks.

ENGINEERING AND THERAPEUTIC APPLICATIONS OF MICROTUBULES

2011 ◽  
Vol 10 (04n05) ◽  
pp. 873-881
Author(s):  
SONIA KAPOOR ◽  
P. RANJITH ◽  
DULAL PANDA
Keyword(s):  
Cell Division ◽  
Anticancer Agents ◽  
Natural Environment ◽  
Living Cell ◽  
Drug Targets ◽  
Biological Properties ◽  
Self Organization ◽  
Therapeutic Drug ◽  
Therapeutic Applications ◽  
Living Organisms

Living organisms are fascinating systems. The macromolecules that make up a living cell possess equally astounding structural and functional characteristics. By taking simple cues from how these biopolymers organize and work inside the cell, one can draw inspiration to utilize them outside their natural environment for several purposes. Microtubules are example of biopolymers that demonstrate extraordinary properties of hierarchical self-organization, dynamic remodeling and mechanical rigidity. Mimicking the principles and properties of microtubules and improving them have opened novel engineering avenues. In addition, due to the functions that microtubules perform during cell division, they are excellent therapeutic drug targets for anticancer agents. In this work, we describe the biological properties and functions of microtubules, and discuss their engineering and therapeutic applications.

scholarly journals Molecular and Comparative Genetics of Mental Retardation

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 835-881 ◽  
Author(s):  
Jennifer K Inlow ◽  
Linda L Restifo
Keyword(s):  
Mental Retardation ◽  
Homo Sapiens ◽  
System Development ◽  
Laboratory Data ◽  
Fruit Fly ◽  
Mendelian Inheritance ◽  
Nervous System Development ◽  
Skewed Distribution ◽  
Therapeutic Drug ◽  
Cellular Mechanisms

Abstract Affecting 1-3% of the population, mental retardation (MR) poses significant challenges for clinicians and scientists. Understanding the biology of MR is complicated by the extraordinary heterogeneity of genetic MR disorders. Detailed analyses of >1000 Online Mendelian Inheritance in Man (OMIM) database entries and literature searches through September 2003 revealed 282 molecularly identified MR genes. We estimate that hundreds more MR genes remain to be identified. A novel test, in which we distributed unmapped MR disorders proportionately across the autosomes, failed to eliminate the well-known X-chromosome overrepresentation of MR genes and candidate genes. This evidence argues against ascertainment bias as the main cause of the skewed distribution. On the basis of a synthesis of clinical and laboratory data, we developed a biological functions classification scheme for MR genes. Metabolic pathways, signaling pathways, and transcription are the most common functions, but numerous other aspects of neuronal and glial biology are controlled by MR genes as well. Using protein sequence and domain-organization comparisons, we found a striking conservation of MR genes and genetic pathways across the ∼700 million years that separate Homo sapiens and Drosophila melanogaster. Eighty-seven percent have one or more fruit fly homologs and 76% have at least one candidate functional ortholog. We propose that D. melanogaster can be used in a systematic manner to study MR and possibly to develop bioassays for therapeutic drug discovery. We selected 42 Drosophila orthologs as most likely to reveal molecular and cellular mechanisms of nervous system development or plasticity relevant to MR.

scholarly journals 4E Interacting Protein as a Potential Novel Drug Target for Nucleoside Analogues in Trypanosoma Brucei

2021 ◽  
Vol 9 (4) ◽  
pp. 826
Author(s):  
Dorien Mabille ◽  
Camila Cardoso Santos ◽  
Rik Hendrickx ◽  
Mathieu Claes ◽  
Peter Takac ◽  
...  
Keyword(s):  
Mode Of Action ◽  
Drug Target ◽  
Drug Targets ◽  
De Novo ◽  
Treatment Options ◽  
Adenosine Kinase ◽  
Nucleoside Analogues ◽  
Purine Salvage ◽  
Interacting Protein ◽  
Novel Drug

Human African trypanosomiasis is a neglected parasitic disease for which the current treatment options are quite limited. Trypanosomes are not able to synthesize purines de novo and thus solely depend on purine salvage from the host environment. This characteristic makes players of the purine salvage pathway putative drug targets. The activity of known nucleoside analogues such as tubercidin and cordycepin led to the development of a series of C7-substituted nucleoside analogues. Here, we use RNA interference (RNAi) libraries to gain insight into the mode-of-action of these novel nucleoside analogues. Whole-genome RNAi screening revealed the involvement of adenosine kinase and 4E interacting protein into the mode-of-action of certain antitrypanosomal nucleoside analogues. Using RNAi lines and gene-deficient parasites, 4E interacting protein was found to be essential for parasite growth and infectivity in the vertebrate host. The essential nature of this gene product and involvement in the activity of certain nucleoside analogues indicates that it represents a potential novel drug target.

Developing novel chemical entities for the treatment of lysosomal storage disorders: an academic perspective

2015 ◽  
Vol 309 (12) ◽  
pp. F996-F999 ◽  
Author(s):  
James A. Shayman
Keyword(s):  
Drug Targets ◽  
Lysosomal Storage ◽  
Federal Drug Administration ◽  
Drug Candidates ◽  
Gaucher Disease Type 1 ◽  
Biotechnology Companies ◽  
Approved Drugs ◽  
Novel Drug ◽  
Early Drug

Historically, most Federal Drug Administration-approved drugs were the result of “in-house” efforts within large pharmaceutical companies. Over the last two decades, this paradigm has steadily shifted as the drug industry turned to startups, small biotechnology companies, and academia for the identification of novel drug targets and early drug candidates. This strategic pivot has created new opportunities for groups less traditionally associated with the creation of novel therapeutics, including small academic laboratories, for engagement in the drug discovery process. A recent example of the successful development of a drug that had its origins in academia is eliglustat tartrate, an oral agent for Gaucher disease type 1.

scholarly journals Mining Significant Substructure Pairs for Interpreting Polypharmacology in Drug-Target Network

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e16999 ◽  
Author(s):  
Ichigaku Takigawa ◽  
Koji Tsuda ◽  
Hiroshi Mamitsuka
Keyword(s):  
Drug Target ◽  
Target Network

scholarly journals Drug Target Prediction Based on the Herbs Components: The Study on the Multitargets Pharmacological Mechanism of Qishenkeli Acting on the Coronary Heart Disease

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Yong Wang ◽  
Zhongyang Liu ◽  
Chun Li ◽  
Dong Li ◽  
Yulin Ouyang ◽  
...  
Keyword(s):  
Coronary Heart Disease ◽  
Heart Disease ◽  
Angiotensin Ii ◽  
Drug Target ◽  
Drug Targets ◽  
Target Prediction ◽  
Coronary Artery Ligation ◽  
Potential Drug ◽  
Drug Target Prediction ◽  
Potential Drug Targets

In this paper, we present a case study of Qishenkeli (QSKL) to research TCM’s underlying molecular mechanism, based on drug target prediction and analyses of TCM chemical components and following experimental validation. First, after determining the compositive compounds of QSKL, we use drugCIPHER-CS to predict their potential drug targets. These potential targets are significantly enriched with known cardiovascular disease-related drug targets. Then we find these potential drug targets are significantly enriched in the biological processes of neuroactive ligand-receptor interaction, aminoacyl-tRNA biosynthesis, calcium signaling pathway, glycine, serine and threonine metabolism, and renin-angiotensin system (RAAS), and so on. Then, animal model of coronary heart disease (CHD) induced by left anterior descending coronary artery ligation is applied to validate predicted pathway. RAAS pathway is selected as an example, and the results show that QSKL has effect on both rennin and angiotensin II receptor (AT1R), which eventually down regulates the angiotensin II (AngII). Bioinformatics combing with experiment verification can provide a credible and objective method to understand the complicated multitargets mechanism for Chinese herbal formula.

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